Changes between Version 106 and Version 107 of SOPs/atac_Seq

Timestamp:

04/03/24 14:23:30 (9 months ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -6 +6 @@
 
 === Basic Approach ===
- * [#preprocess Pre-process reads] (remove adapters and other "contamination")
- * [#map Map reads to the genome, and post-alignment filtering]
- * [#postAlignQC Post-alignment quality control and calculate QC metrics]
- * [#call_peaks Call ATAC-seq "peaks"] with a high coverage of mapped reads
- * [#AfterPeakQC Quality control after calling peaks]
- * [#Blacklist Blacklist filtering for peaks ] 
- * [#QC Run quality control and calculate QC metrics] 
- * [#Analyze Analyze peak regions for binding motifs]
- * Identify differentially accessible regions (for multiple-sample experiments)
- * Identify potential targets of peak regions and/or differentially accessible regions
 
 If your samples consist of human or mouse specimens with biological replicates, you can execute the ENCODE pipeline seamlessly, encompassing steps 1 through 7 in a single run.
+
+
+ 1. [#preprocess Pre-process reads] (remove adapters and other "contamination")
+
+ 2. [#map Map reads to the genome, and post-alignment filtering]
+
+ 3. [#postAlignQC Post-alignment quality control and calculate QC metrics]
+
+ 4. [#call_peaks Call ATAC-seq "peaks"] with a high coverage of mapped reads
+
+ 5. [#AfterPeakQC Quality control after calling peaks]
+
+ 6. [#Blacklist Blacklist filtering for peaks ] 
+
+ 7. [#QC Run quality control and calculate QC metrics] 
+
+ 8. [#Analyze Analyze peak regions for binding motifs]
+
+ 9. Identify differentially accessible regions (for multiple-sample experiments)
+
+ 10. Identify potential targets of peak regions and/or differentially accessible regions
+
+
 
 === [=#preprocess Pre-process reads] ===